Publications – Center for Communicable Disease Dynamics

Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: a malaria case study.

Author(s): LaVerriere E, Schwabl P, Carrasquilla M, Taylor AR, Johnson ZM, Shieh M, Panchal R, Straub TJ, Kuzma R, Watson S, Buckee CO, Andrade CM, Portugal S, Crompton PD, Traore B, Rayner JC, Corredor V, James K, Cox H, Early AM, MacInnis BL, Neafsey DEJournal: Mol Ecol ResourPMID: 35437908 April 2022

Multiplexed PCR amplicon sequencing (AmpSeq) is an increasingly popular application for cost-effective monitoring of threatened species and managed wildlife populations,…

Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis

Author(s): Carrasquilla M, Early AM, Taylor AR, Knudson A, Echeverry DF, Anderson TJ, Mancilla E, Aponte S, Cárdenas P, Buckee CO, Rayner JC, Sáenz FE, Neafsey DE, Corredor VJournal: bioRxiv February 2022

The human malaria parasite Plasmodium falciparum is globally widespread, but its prevalence varies significantly between and even within countries. Most…

Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast.

Author(s): Taylor AR, Echeverry DF, Anderson TJC, Neafsey DE, Buckee COJournal: PLoS GenetPMID: 33196661 November 2020

Characterising connectivity between geographically separated biological populations is a common goal in many fields. Recent approaches to understanding connectivity between…

Resolving the cause of recurrent Plasmodium vivax malaria probabilistically.

Author(s): Taylor AR, Watson JA, Chu CS, Puaprasert K, Duanguppama J, Day NPJ, Nosten F, Neafsey DE, Buckee CO, Imwong M, White NJJournal: Nat CommunPMID: 31811128 December 2019

Relapses arising from dormant liver-stage Plasmodium vivax parasites (hypnozoites) are a major cause of vivax malaria. However, in endemic areas,…

Estimating Relatedness Between Malaria Parasites.

Author(s): Taylor AR, Jacob PE, Neafsey DE, Buckee COJournal: GeneticsPMID: 31209105 August 2019

Understanding the relatedness of individuals within or between populations is a common goal in biology. Increasingly, relatedness features in genetic…

Correction to: Mapping malaria by combining parasite genomic and epidemiologic data.

Author(s): Wesolowski A, Taylor AR, Chang HH, Verity R, Tessema S, Bailey JA, Alex Perkins T, Neafsey DE, Greenhouse B, Buckee COJournal: BMC MedPMID: 30591060 December 2018

The original article [1] contained an error in the presentation of Figure 1; this error has now been rectified and…

Mapping malaria by combining parasite genomic and epidemiologic data.

Author(s): Wesolowski A, Taylor AR, Chang HH, Verity R, Tessema S, Bailey JA, Alex Perkins T, Neafsey DE, Greenhouse B, Buckee COJournal: BMC MedPMID: 30333020 October 2018

Recent global progress in scaling up malaria control interventions has revived the goal of complete elimination in many countries. Decreasing…

Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent.

Author(s): Taylor AR, Schaffner SF, Cerqueira GC, Nkhoma SC, Anderson TJC, Sriprawat K, Pyae Phyo A, Nosten F, Neafsey DE, Buckee COJournal: PLoS GenetPMID: 29077712 October 2017

With the rapidly increasing abundance and accessibility of genomic data, there is a growing interest in using population genetic approaches…

THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites.

Author(s): Chang HH, Worby CJ, Yeka A, Nankabirwa J, Kamya MR, Staedke SG, Dorsey G, Murphy M, Neafsey DE, Jeffreys AE, Hubbart C, Rockett KA, Amato R, Kwiatkowski DP, Buckee CO, Greenhouse BJournal: PLoS Comput BiolPMID: 28125584 January 2017

As many malaria-endemic countries move towards elimination of Plasmodium falciparum, the most virulent human malaria parasite, effective tools for monitoring…

Immune characterization of Plasmodium falciparum parasites with a shared genetic signature in a region of decreasing transmission.

Author(s): Bei AK, Diouf A, Miura K, Larremore DB, Ribacke U, Tullo G, Moss EL, Neafsey DE, Daniels RF, Zeituni AE, Nosamiefan I, Volkman SK, Ahouidi AD, Ndiaye D, Dieye T, Mboup S, Buckee CO, Long CA, Wirth DFJournal: Infect ImmunPMID: 25368109 January 2015

As the intensity of malaria transmission has declined, Plasmodium falciparum parasite populations have displayed decreased clonal diversity resulting from the…